Introduction to Docker and Singularity

Introduction to Docker
8 Topics
Background about Docker
Docker components
Docker vocabulary
Container Setup explained
Basics of the Docker images
What is Containerization?
Advantages of Docker
Typical use cases
Using existing images
13 Topics
Explore Docker hub
Exercise on getting images
Get tools from Biocontainers
List docker images
Starting an image with docker run
Run container as daemon
Check containers status via docker ps
Clean up the containers and the images
Execute a process in running container
Summary
Volumes
Excercise with volumes
Ports
Docker recipes: build your own images
12 Topics
Building the recipes for images
More advanced image building
Building cache
Tagging the images
Starting the build
More instructions for the recipes
One tool, one image or some tools, one image
General recommendations
Dockerfile tips
Getting an image to Docker Hub
Inspecting Dockerfiles created by other parties
Using Biocontainers and Bioconda for bioinformatics tools
Introduction to Singularity
6 Topics
Background about Singularity
Strengths and Weaknesses
Singularity Architecture
Getting started
Singularity’s Image Cache
Using existing Singularity images
Run and execute Singularity images
6 Topics
Using the Singularity containers to run commands
Files in Singularity containers
Binding local folders (aka volumes)
Using Docker images with Singularity
Run from sandbox container or remotely
Troubleshooting options
Building Singularity images
4 Topics
Building Singularity images
Change the image via sandbox
Using singularity recipes
Remotely building
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Starting the build

Introduction to Docker and Singularity Docker recipes: build your own images Starting the build

Implicitely looks for a Dockerfile file in the current directory:

docker build .
docker build --file Dockerfile .

Syntax: –file / -f

. stands for the context (in this case, current directory) of the build process. This makes sense if copying files from filesystem, for instance. IMPORTANT: Avoid contexts (directories) overpopulated with files (even if not actually used in the recipe).

You can define a specific name for the image during the build process.

Syntax: -t imagename:tag. If not defined :tag default is latest.

docker build -t mytestimage .

The last line of installation should be Successfully built …: then you are good to go.
Check with docker images that you see the newly built image in the list…

Then let’s check the ID of the image and run it!

docker images

docker run f9f41698e2f8
docker run mytestimage
docker run f9f41698e2f8 https://cdn-images-1.medium.com/max/1600/1*_NQN6_YnxS29m8vFzWYlEg.png
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